LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# thermostatting 2 regions via fix langevin

# settings

variable	x equal 10
variable	y equal 10
variable	z equal 20

variable	rho equal 0.6
variable        t equal 1.35
variable	rc equal 2.5
variable        tlo equal 1.0
variable        thi equal 1.70

#variable	rho equal 0.85
#variable        t equal 0.7
#variable	rc equal 3.0
#variable        tlo equal 0.3
#variable        thi equal 1.0

# setup problem

units		lj
atom_style	atomic

lattice		fcc ${rho}
lattice		fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region		box block 0 $x 0 $y 0 $z
region		box block 0 10 0 $y 0 $z
region		box block 0 10 0 10 0 $z
region		box block 0 10 0 10 0 20
create_box	1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
  2 by 1 by 4 MPI processor grid
create_atoms	1 box
Created 8000 atoms
mass		1 1.0

velocity	all create $t 87287
velocity	all create 1.35 87287

pair_style	lj/cut ${rc}
pair_style	lj/cut 2.5
pair_coeff	1 1 1.0 1.0

neighbor	0.3 bin
neigh_modify	delay 0 every 1

# heat layers

region          hot block INF INF INF INF 0 1
region          cold block  INF INF INF INF 10 11
compute         Thot all temp/region hot
compute         Tcold all temp/region cold

# 1st equilibration run

fix             1 all nvt temp $t $t 0.5
fix             1 all nvt temp 1.35 $t 0.5
fix             1 all nvt temp 1.35 1.35 0.5
thermo	        100
run             1000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 14 14 27
Memory usage per processor = 2.55761 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
     800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
     900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
    1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
Loop time of 0.876399 on 8 procs for 1000 steps with 8000 atoms

Performance: 492926.111 tau/day, 1141.033 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.47963    | 0.4975     | 0.51846    |   1.6 | 56.77
Neigh   | 0.22878    | 0.23186    | 0.23458    |   0.4 | 26.46
Comm    | 0.081789   | 0.096763   | 0.11865    |   3.6 | 11.04
Output  | 0.000247   | 0.00025409 | 0.00028944 |   0.1 |  0.03
Modify  | 0.02689    | 0.033982   | 0.042612   |   2.9 |  3.88
Other   |            | 0.01604    |            |       |  1.83

Nlocal:    1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost:    2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs:    27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1

Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0

velocity	all scale $t
velocity	all scale 1.35

unfix		1

# 2nd equilibration run

fix		1 all nve
fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix             cold all langevin 1 1 1.0 287859 tally yes
fix_modify      hot temp Thot
fix_modify      cold temp Tcold

variable        tdiff equal c_Thot-c_Tcold
thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
thermo	        1000
run             10000
Memory usage per processor = 3.30761 Mbytes
Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff 
    1000         1.35     1.431295    1.2955644           -0           -0   0.13573065 
    2000    1.3593243    1.6602094    1.0898701  -0.13903162   0.14234352   0.57033928 
    3000    1.3412163    1.6308839    1.0677742   -0.2214765   0.25871329   0.56310968 
    4000    1.3275359    1.5248034    1.0792345  -0.26908328   0.34211202   0.44556887 
    5000    1.3230922    1.6266046    1.0523802  -0.33175886   0.43533756    0.5742244 
    6000    1.3037036    1.6021737    1.0408166   -0.3639815   0.49869333   0.56135712 
    7000    1.2903225    1.5701119    1.0603548  -0.40000421   0.55547714   0.50975712 
    8000    1.3050677    1.6420218    1.0221774  -0.46368839   0.60293974   0.61984444 
    9000    1.2950977    1.7153984    1.0583242  -0.51871512   0.66389344   0.65707419 
   10000    1.3100216    1.6680668    1.0871293  -0.57485359    0.7161839   0.58093752 
   11000     1.297052    1.6486494     1.088903  -0.60276081   0.75900024   0.55974633 
Loop time of 11.5988 on 8 procs for 10000 steps with 8000 atoms

Performance: 372451.299 tau/day, 862.156 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.0544     | 4.9719     | 5.8426     |  34.5 | 42.87
Neigh   | 2.0735     | 2.3933     | 2.7208     |  18.8 | 20.63
Comm    | 0.91559    | 1.9788     | 3.1216     |  70.5 | 17.06
Output  | 0.0005753  | 0.00068495 | 0.00080419 |   0.3 |  0.01
Modify  | 1.9354     | 1.9837     | 2.0321     |   2.6 | 17.10
Other   |            | 0.2705     |            |       |  2.33

Nlocal:    1000 ave 1112 max 841 min
Histogram: 1 1 0 2 0 0 0 0 1 3
Nghost:    2294.38 ave 2506 max 2077 min
Histogram: 2 1 1 0 0 0 0 1 1 2
Neighs:    27441.9 ave 32651 max 19438 min
Histogram: 1 1 0 2 0 0 0 0 0 4

Total # of neighbors = 219535
Ave neighs/atom = 27.4419
Neighbor list builds = 1674
Dangerous builds = 0

# thermal conductivity calculation
# reset langevin thermostats to zero energy accumulation

compute		ke all ke/atom
variable	temp atom c_ke/1.5

fix             hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix             hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix             hot all langevin 1.7 1.7 1.0 59804 tally yes
fix             cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix             cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix             cold all langevin 1 1 1.0 287859 tally yes
fix_modify      hot temp Thot
fix_modify      cold temp Tcold

fix             ave all ave/time 10 100 1000 v_tdiff ave running
thermo_style    custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave

compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin

run             20000
Memory usage per processor = 3.5578 Mbytes
Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave 
   11000     1.297052    1.6473904     1.088903           -0           -0   0.55848738            0 
   12000    1.2792808    1.6043738    1.0658375 -0.012256975   0.04611547   0.53853632   0.54492428 
   13000    1.2787101    1.7035572    1.1159037 -0.073806664  0.099529002   0.58765348    0.5581748 
   14000     1.289918    1.4642237    1.1073937  -0.11428779   0.13931657   0.35683005   0.56816328 
   15000    1.2932964    1.5032665    1.0523148  -0.17247717   0.19001309   0.45095174   0.57436291 
   16000    1.3025037    1.5424316    1.1185175  -0.22598282   0.22640921   0.42391405   0.56973168 
   17000    1.3009667    1.5582105    1.0745661  -0.27544101   0.26143452   0.48364439    0.5700118 
   18000    1.2970255    1.5019842    1.0228322  -0.31195285   0.31203237     0.479152   0.56544644 
   19000    1.2880631    1.5290587    1.0976483  -0.34645573   0.34243366   0.43141047   0.56338309 
   20000    1.3119675    1.6284144    1.1102294  -0.40922326   0.39217092   0.51818503   0.56614474 
   21000    1.2838063    1.6670934   0.97721382  -0.43809329   0.46021572   0.68987962    0.5686161 
   22000    1.2925041    1.7050682    1.0984963   -0.4871305   0.50520177    0.6065719   0.57226368 
   23000    1.2746463    1.6388503    1.0286701  -0.51212873   0.56478515    0.6101802   0.57290996 
   24000    1.2745381    1.7085713    1.1362975  -0.54529463   0.58540408   0.57227375   0.57296767 
   25000    1.2776401    1.5259253    1.0415158  -0.58389862   0.62623289   0.48440948   0.57386374 
   26000    1.2661888    1.4760829   0.99145001  -0.62638032   0.68155754   0.48463289   0.57021631 
   27000    1.2923677    1.6070495    1.0300276  -0.70014343   0.70236265    0.5770219   0.57001637 
   28000    1.2961449    1.7052335    1.0805793  -0.74856241   0.75775659   0.62465427   0.56927907 
   29000    1.2969474    1.5520176    1.1249649  -0.78900962   0.79539202   0.42705264   0.56986986 
   30000    1.2900596    1.6556864    1.0302676  -0.84180996   0.87187683    0.6254189   0.57245841 
   31000    1.2923209    1.6752068    1.0156911  -0.89036148   0.88285227   0.65951571   0.57358134 
Loop time of 24.1059 on 8 procs for 20000 steps with 8000 atoms

Performance: 358418.039 tau/day, 829.671 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.5967     | 9.9644     | 12.189     |  62.9 | 41.34
Neigh   | 3.9305     | 4.7817     | 5.594      |  34.5 | 19.84
Comm    | 1.7656     | 4.5624     | 7.6382     | 122.3 | 18.93
Output  | 0.0011697  | 0.0018933  | 0.0020008  |   0.6 |  0.01
Modify  | 4.1386     | 4.2107     | 4.3622     |   3.8 | 17.47
Other   |            | 0.5848     |            |       |  2.43

Nlocal:    1000 ave 1118 max 875 min
Histogram: 2 1 1 0 0 0 0 0 2 2
Nghost:    2298.62 ave 2535 max 2063 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs:    27462.4 ave 32904 max 21333 min
Histogram: 2 2 0 0 0 0 0 0 0 4

Total # of neighbors = 219699
Ave neighs/atom = 27.4624
Neighbor list builds = 3340
Dangerous builds = 0
Total wall time: 0:00:36
